load_all() does not activate S4 dispatch for methods on ...-dispatching base generics (e.g. seq)

[programLyrique]

Context

I develop a mutation testing package for R (mutator) and it uses pkgload to quickly reload the package for each of the test suite runs it has to perform (can be 1000s of them). I have system tests that compare results between running a test suite with pkgload or running it with R CMD INSTALL (so installing the package each time) and they caught a discrepancy for package nanotime (0.3.15) on S4 dispatches.

Its tinytest suite calls seq(<nanoival>, by = <nanoperiod>, length.out = ...), which under load_all() falls to seq.default and then hits nanotime's deliberately-disabled + for those types:

binary '+' is not defined for 'nanoival' and 'nanoperiod' objects; instead use 'plus(e1, e2, tz)'

Summary

When a package defines an S4 method on a base generic that dispatches on ... (the clearest example is seq, whose implicit generic has signature "..."), the method is registered correctly under pkgload::load_all() (existsMethod() / selectMethod() find it and it runs when invoked directly), but normal dispatch does not reach it as soon as the call has more than one argument. R silently falls through to the internal default (seq.default).

The exact same package installed (R CMD INSTALL + library()) dispatches correctly for any number of arguments. Hence, a load_all()/methods setup issue, not a problem with the package.

• seq(x) (single argument): S4 method is dispatched
• seq(x, by = 1L, length.out = 3) (extra args): falls to seq.default (only under load_all())

Minimal reprex

# Build a tiny package: one S4 class with an S4 method on `seq`.
d <- file.path(tempfile("s4seq_"), "s4seqpkg")
dir.create(file.path(d, "R"), recursive = TRUE)
writeLines(
  "Package: s4seqpkg\nVersion: 0.1.0\nTitle: T\nDescription: d.\nAuthor: A\nLicense: MIT\nImports: methods",
  file.path(d, "DESCRIPTION")
)
writeLines(
  c("import(methods)", "exportClasses(myc)", "exportMethods(seq)"),
  file.path(d, "NAMESPACE")
)
writeLines(
  c(
    "setClass('myc', contains = 'numeric')",
    "setMethod('seq', 'myc', function(from, ...) 99L)"
  ),
  file.path(d, "R", "x.R")
)

## --- via pkgload::load_all() ---------------------------------------------
pkgload::load_all(d, quiet = TRUE)
b <- new("myc", 1)

seq(b)                              #> [1] 99      (S4 method dispatched)
seq(b, by = 1L, length.out = 3)    #> [1] 1 2 3   (WRONG: seq.default, S4 method skipped)

# The method IS registered and works when invoked explicitly:
existsMethod("seq", "myc")                                  #> [1] TRUE
selectMethod("seq", "myc")(b, by = 1L, length.out = 3)     #> [1] 99

Now the same package installed dispatches correctly:

lib <- tempfile("lib_"); dir.create(lib)
system2(file.path(R.home("bin"), "R"),
        c("CMD", "INSTALL", paste0("--library=", lib), d),
        stdout = FALSE, stderr = FALSE)

# In a fresh session:
.libPaths(c(lib, .libPaths()))
library(s4seqpkg)
b <- new("myc", 1)
seq(b)                             #> [1] 99
seq(b, by = 1L, length.out = 3)    #> [1] 99   (correct: S4 method dispatched)

Some notes

• The method is present after load_all(): isGeneric("seq") is TRUE, existsMethod("seq", "myc") is TRUE, find("seq") shows the package's
  standardGeneric ahead of base, and selectMethod(...)() returns the right answer. Only implicit dispatch through a bare seq(...) call misses it, and only once extra arguments are present.
• It is specific to generics that dispatch on .... S4 methods on generics that dispatch on a named formal work fine under load_all() , for instance, setMethod("mean", "myc", ...) (mean(x, ...)) dispatches correctly.
• It is not about primitives: S4 methods on primitive group generics such as +/Arith dispatch correctly under load_all() (C-level dispatch). This rather happens with internal generics such as seq (function (...) UseMethod("seq")).
• Not fixed by any of: methods::cacheMetaData(ns, TRUE), methods::setGeneric("seq"), or load_all(export_all = FALSE).

Environment

• pkgload 1.5.3
• R 4.6.1 (2026-06-24)
• Platform: Linux (x86_64)
• methods (base)

Related issues

Might be related to #45